#knitr::opts_chunk$set(message = FALSE, echo = FALSE)
library(Matrix)
library(genomation)
## Loading required package: grid
library(matrixStats)
library(knitr)
library(ggplot2)
library(ArchR)
## Loading required package: SummarizedExperiment
## Loading required package: GenomicRanges
## Loading required package: stats4
## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB
## The following object is masked from 'package:Matrix':
## 
##     which
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
##     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
##     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
##     union, unique, unsplit, which, which.max, which.min
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:Matrix':
## 
##     expand
## The following object is masked from 'package:base':
## 
##     expand.grid
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## 
## Attaching package: 'Biobase'
## The following objects are masked from 'package:matrixStats':
## 
##     anyMissing, rowMedians
## Loading required package: DelayedArray
## Loading required package: BiocParallel
## 
## Attaching package: 'DelayedArray'
## The following objects are masked from 'package:matrixStats':
## 
##     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
## The following objects are masked from 'package:base':
## 
##     aperm, apply, rowsum
## Loading required package: data.table
## 
## Attaching package: 'data.table'
## The following object is masked from 'package:SummarizedExperiment':
## 
##     shift
## The following object is masked from 'package:GenomicRanges':
## 
##     shift
## The following object is masked from 'package:IRanges':
## 
##     shift
## The following objects are masked from 'package:S4Vectors':
## 
##     first, second
## Loading required package: rhdf5
## Loading required package: magrittr

Data was preprocessed by Tiffany using the Cell Ranger Pipeline: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/algorithms/overview

Based on marker genes, plots below,

  • Cluster 1-3 express HBC markers
  • Cluster 4 seems to be neuronal (Omp, Cnga2 only expressed in cl4). Seeems split in 2, possibly inhibitory and excitatory?
  • Cluster 5 expresses SUS markers (Cyp2g1).
  • Cluster 6 doesn’t really seem to be consistent and doesnt really express anything so may be low quality cells.
## Setting default genome to Mm10.
## Using GeneAnnotation set by addArchRGenome(Mm10)!
## Using GeneAnnotation set by addArchRGenome(Mm10)!
## Cleaning Temporary Files
## 2020-11-24 21:04:12 : Batch Execution w/ safelapply!, 0 mins elapsed.
## (s1Inj : 1 of 6) Checking if completed file exists!
## 2020-11-24 21:04:12 : (s1Inj : 1 of 6) Arrow Exists! Marking as completed since force = FALSE!, 0.001 mins elapsed.
## (s3Inj : 2 of 6) Checking if completed file exists!
## 2020-11-24 21:04:13 : (s3Inj : 2 of 6) Arrow Exists! Marking as completed since force = FALSE!, 0.002 mins elapsed.
## (s2UI : 3 of 6) Checking if completed file exists!
## 2020-11-24 21:04:13 : (s2UI : 3 of 6) Arrow Exists! Marking as completed since force = FALSE!, 0.002 mins elapsed.
## (s3UI : 4 of 6) Checking if completed file exists!
## 2020-11-24 21:04:13 : (s3UI : 4 of 6) Arrow Exists! Marking as completed since force = FALSE!, 0.002 mins elapsed.
## (s2Inj : 5 of 6) Checking if completed file exists!
## 2020-11-24 21:04:13 : (s2Inj : 5 of 6) Arrow Exists! Marking as completed since force = FALSE!, 0.003 mins elapsed.
## (s1UI : 6 of 6) Checking if completed file exists!
## 2020-11-24 21:04:13 : (s1UI : 6 of 6) Arrow Exists! Marking as completed since force = FALSE!, 0.003 mins elapsed.
## ArchR logging successful to : ../data/scATAC/arrowLogFile.txt
## Using GeneAnnotation set by addArchRGenome(Mm10)!
## Using GeneAnnotation set by addArchRGenome(Mm10)!
## Validating Arrows...
## Getting SampleNames...
## 1 2 3 4 5 6 
## Copying ArrowFiles to Ouptut Directory! If you want to save disk space set copyArrows = FALSE
## 1 2 3 4 5 6 
## Getting Cell Metadata...
## 1 2 3 4 5 6 
## Merging Cell Metadata...
## Initializing ArchRProject...
## 
##                                                    / |
##                                                  /    \
##             .                                  /      |.
##             \\\                              /        |.
##               \\\                          /           `|.
##                 \\\                      /              |.
##                   \                    /                |\
##                   \\#####\           /                  ||
##                 ==###########>      /                   ||
##                  \\##==......\    /                     ||
##             ______ =       =|__ /__                     ||      \\\
##         ,--' ,----`-,__ ___/'  --,-`-===================##========>
##        \               '        ##_______ _____ ,--,__,=##,__   ///
##         ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
##         -,____,---'       \\####\\________________,--\\_##,/
##            ___      .______        ______  __    __  .______      
##           /   \     |   _  \      /      ||  |  |  | |   _  \     
##          /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
##         /  /_\  \   |      /     |  |     |   __   | |      /     
##        /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
##       /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
##     
## ArchR logging to : ArchRLogs/ArchR-addDoubletScores-cca71eb6862e-Date-2020-11-24_Time-21-04-20.log
## If there is an issue, please report to github with logFile!
## 2020-11-24 21:04:20 : Batch Execution w/ safelapply!, 0 mins elapsed.
## Filtering 1 dims correlated > 0.75 to log10(depth + 1)
## s1Inj (1 of 6) : UMAP Projection R^2 = 0.95591
## s1Inj (1 of 6) : UMAP Projection R^2 = 0.95591

## Filtering 1 dims correlated > 0.75 to log10(depth + 1)
## s3Inj (2 of 6) : UMAP Projection R^2 = 0.97708
## s3Inj (2 of 6) : UMAP Projection R^2 = 0.97708
## Filtering 1 dims correlated > 0.75 to log10(depth + 1)
## s3UI (3 of 6) : UMAP Projection R^2 = 0.98534
## s3UI (3 of 6) : UMAP Projection R^2 = 0.98534
## Filtering 1 dims correlated > 0.75 to log10(depth + 1)
## s2UI (4 of 6) : UMAP Projection R^2 = 0.93469
## s2UI (4 of 6) : UMAP Projection R^2 = 0.93469
## s2Inj (5 of 6) : UMAP Projection R^2 = 0.91338
## s2Inj (5 of 6) : UMAP Projection R^2 = 0.91338
## s1UI (6 of 6) : UMAP Projection R^2 = 0.77624
## s1UI (6 of 6) : UMAP Projection R^2 = 0.77624
## s1UI (6 of 6) : Correlation of UMAP Projection is below 0.9 (normally this is ~0.99)
## This means there is little heterogeneity in your sample and thus doubletCalling is inaccurate.
## force = FALSE, thus returning -1 doubletScores and doubletEnrichments!
## Set force = TRUE if you want to contniue (not recommended).
## s1UI (6 of 6) : Correlation of UMAP Projection is below 0.9 (normally this is ~0.99)
## This means there is little heterogeneity in your sample and thus doubletCalling is inaccurate.
## force = FALSE, thus returning -1 doubletScores and doubletEnrichments!
## Set force = TRUE if you want to contniue (not recommended).
## ArchR logging successful to : ArchRLogs/ArchR-addDoubletScores-cca71eb6862e-Date-2020-11-24_Time-21-04-20.log
## Checking Inputs...
## ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-cca711178f15-Date-2020-11-24_Time-21-10-35.log
## If there is an issue, please report to github with logFile!
## 2020-11-24 21:10:35 : Computing Total Accessibility Across All Features, 0.003 mins elapsed.
## 2020-11-24 21:10:37 : Computing Top Features, 0.042 mins elapsed.
## ###########
## 2020-11-24 21:10:38 : Running LSI (1 of 2) on Top Features, 0.046 mins elapsed.
## ###########
## 2020-11-24 21:10:38 : Creating Partial Matrix, 0.046 mins elapsed.
## 2020-11-24 21:10:59 : Computing LSI, 0.406 mins elapsed.
## 2020-11-24 21:11:16 : Identifying Clusters, 0.689 mins elapsed.
## 2020-11-24 21:11:25 : Identified 5 Clusters, 0.841 mins elapsed.
## 2020-11-24 21:11:25 : Saving LSI Iteration, 0.841 mins elapsed.
## 2020-11-24 21:11:39 : Creating Cluster Matrix on the total Group Features, 1.068 mins elapsed.
## 2020-11-24 21:12:18 : Computing Variable Features, 1.717 mins elapsed.
## ###########
## 2020-11-24 21:12:18 : Running LSI (2 of 2) on Variable Features, 1.719 mins elapsed.
## ###########
## 2020-11-24 21:12:18 : Creating Partial Matrix, 1.719 mins elapsed.
## 2020-11-24 21:12:33 : Computing LSI, 1.964 mins elapsed.
## 2020-11-24 21:12:43 : Finished Running IterativeLSI, 2.137 mins elapsed.
## ArchR logging to : ArchRLogs/ArchR-addClusters-cca760796e0-Date-2020-11-24_Time-21-12-47.log
## If there is an issue, please report to github with logFile!
## plots: batch correction
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "Sample", embedding = "UMAP_cor")
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca760cb1d73-Date-2020-11-24_Time-21-13-06.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca760cb1d73-Date-2020-11-24_Time-21-13-06.log
p4 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "clusters_cor", embedding = "UMAP_cor")
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca736fa9aaa-Date-2020-11-24_Time-21-13-06.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca736fa9aaa-Date-2020-11-24_Time-21-13-06.log
ggAlignPlots(p3, p4, type = "h")

Distribution of samples within clusters, and marker genes.

## Getting ImputeWeights
## No imputeWeights found, returning NULL
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca77a4d75aa-Date-2020-11-24_Time-21-13-09.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = GeneScoreMatrix
## Getting Matrix Values...
## 2020-11-24 21:13:09 :
## 1 2 3 4 5 6 
## Plotting Embedding
## 1 2 3 4 5 6 7 8 9 10 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca77a4d75aa-Date-2020-11-24_Time-21-13-09.log
## $OMP

## 
## $ASCL1

## 
## $NEUROD1

## 
## $KRT5

## 
## $KRT14

## 
## $TRP63

## 
## $KRTDAP

## 
## $SPRR1A

## 
## $CYP2G1

## 
## $CYP1A2

DA analysis on gene scores, comparing injured vs non-injured HBCs

## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca73bc6a991-Date-2020-11-24_Time-21-13-20.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca73bc6a991-Date-2020-11-24_Time-21-13-20.log

Plots for paper on full dataset

library(ggplot2)
plotEmbedding(ArchRProj = proj, 
              colorBy = "cellColData", 
              name = "clMerged", 
              embedding = "UMAP_cor")
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca71f835c5d-Date-2020-11-24_Time-21-13-22.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca71f835c5d-Date-2020-11-24_Time-21-13-22.log

umapDims <- ArchR::getEmbedding(proj, "UMAP_cor")
colnames(umapDims) <- c("UMAP1", "UMAP2")
umapDims$clMerged <- getCellColData(proj, select = "clMerged")$clMerged
umapDims$clMerged[umapDims$clMerged == "Neur"] <- "Neuronal"
umapDims$clMerged[umapDims$clMerged == "Sus"] <- "Sustentacular"

pCellType <- ggplot(umapDims, aes(x=UMAP1, y=UMAP2, color=clMerged)) +
  geom_point(size = 1) + 
  theme_classic() +
  labs(color = "Cell type")

pCellType

Preliminary HBC analysis without integration

## select cells for DA
nCells(proj)
## [1] 4732
proj <- proj[which(clMerged == "HBC"),]
proj <- addUMAP(ArchRProj = proj, reducedDims = "Harmony", force=TRUE, name="UMAP_cor",
  verbose = FALSE)
plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "clMerged", embedding = "UMAP_cor")
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca75a5268c2-Date-2020-11-24_Time-21-13-34.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca75a5268c2-Date-2020-11-24_Time-21-13-34.log

hbcInj <- vector(length=nCells(proj))
hbcInj[proj@cellColData$treat == "Inj"] <- "hbc_inj"
hbcInj[proj@cellColData$treat == "UI"] <- "hbc_uninj"
proj@cellColData$hbcInj <- hbcInj
plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "hbcInj", embedding = "UMAP_cor")
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca7585bc6e1-Date-2020-11-24_Time-21-13-35.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca7585bc6e1-Date-2020-11-24_Time-21-13-35.log

markerRes <- getMarkerFeatures(
    ArchRProj = proj, 
    useMatrix = "GeneScoreMatrix", 
    groupBy = "hbcInj",
    bias = c("TSSEnrichment", "log10(nFrags)"),
    testMethod = "wilcoxon",
  verbose = FALSE)
## ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-cca7715e0b18-Date-2020-11-24_Time-21-13-36.log
## If there is an issue, please report to github with logFile!
## MatrixClass = Sparse.Double.Matrix
## ArchR logging successful to : ArchRLogs/ArchR-getMarkerFeatures-cca7715e0b18-Date-2020-11-24_Time-21-13-36.log
markerList <- getMarkers(markerRes, cutOff = "FDR <= 0.01 & Log2FC >= 1.25")
heatmapMarkers <- plotMarkerHeatmap(
  seMarker = markerRes, 
  labelMarkers = markers,
  cutOff = "FDR <= 0.01 & Log2FC >= 1.25", 
  transpose = TRUE
)
## ArchR logging to : ArchRLogs/ArchR-plotMarkerHeatmap-cca7552a8ecd-Date-2020-11-24_Time-21-14-17.log
## If there is an issue, please report to github with logFile!
## Printing Top Marker Genes:
## hbc_inj:
##  Prss39, Cfc1, Cnga3, Lyg1, Cxcr2, Dnajb3, Ugt1a1, Mir6345, Serpinb2, Htr5b, Il24, Il20, Scarna3a, 4930562F07Rik, Cd48, Ifi211, Mndal, Ifi205, Olfr433, Olfr432
## hbc_uninj:
##  Jsrp1, Msrb3, Fscn2, Lrrc18, Gm16835, Fam135b, Tectb, Gbp7, Oas1c, Cox8b, Ces1b, Mir328, Prss39, Cfc1, Cnga3, Lyg1, Cxcr2, Dnajb3, Ugt1a1, Mir6345
## Identified 212 markers!
## Adding Annotations..
## ArchR logging successful to : ArchRLogs/ArchR-plotMarkerHeatmap-cca7552a8ecd-Date-2020-11-24_Time-21-14-17.log
# ComplexHeatmap::draw(heatmapMarkers, heatmap_legend_side = "bot", annotation_legend_side = "bot")

Manually merge HBC clusters

plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "clusters_cor", embedding = "UMAP_cor")
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca77de9e8b8-Date-2020-11-24_Time-21-14-18.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca77de9e8b8-Date-2020-11-24_Time-21-14-18.log

plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "hbcInj", embedding = "UMAP_cor")
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca77adc89d-Date-2020-11-24_Time-21-14-19.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca77adc89d-Date-2020-11-24_Time-21-14-19.log

clHBCMerged <- as.character(proj@cellColData$clusters_cor)
clHBCMerged[clHBCMerged %in% c("C3", "C4")] <- "C1_Inj"
clHBCMerged[clHBCMerged %in% c("C9", "C10")] <- "C2_Hybrid"
clHBCMerged[clHBCMerged %in% c("C6", "C7", "C8")] <- "C3_UI"
proj@cellColData$clHBCMerged <- clHBCMerged
plotEmbedding(ArchRProj = proj, colorBy = "cellColData", name = "clHBCMerged", embedding = "UMAP_cor")
## ArchR logging to : ArchRLogs/ArchR-plotEmbedding-cca7224dbf5b-Date-2020-11-24_Time-21-14-20.log
## If there is an issue, please report to github with logFile!
## Getting UMAP Embedding
## ColorBy = cellColData
## Plotting Embedding
## 1 
## ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-cca7224dbf5b-Date-2020-11-24_Time-21-14-20.log

df <- data.frame(cl=proj$clHBCMerged,
                 treatment=proj$treat)

pBar <- ggplot(df, aes(x=treatment, fill=treatment)) + 
  geom_bar(stat="count") +
  facet_wrap(.~cl)
pBar

markerHBCCl <- getMarkerFeatures(
    ArchRProj = proj, 
    useMatrix = "GeneScoreMatrix", 
    groupBy = "clHBCMerged",
    bias = c("TSSEnrichment", "log10(nFrags)"),
    testMethod = "wilcoxon",
  verbose = FALSE)
## ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-cca71e4e00f5-Date-2020-11-24_Time-21-14-21.log
## If there is an issue, please report to github with logFile!
## MatrixClass = Sparse.Double.Matrix
## ArchR logging successful to : ArchRLogs/ArchR-getMarkerFeatures-cca71e4e00f5-Date-2020-11-24_Time-21-14-21.log
markerList_HBCCl <- getMarkers(markerHBCCl, cutOff = "FDR <= 0.01 & Log2FC >= 1.25")
# saveRDS(markerList_HBCCl, file="../data/markerList_atac_ArchR_hbcClusters.rds")

heatmapMarkers <- plotMarkerHeatmap(
  seMarker = markerHBCCl, 
  labelMarkers = markers,
  cutOff = "FDR <= 0.01 & Log2FC >= 1.25", 
  transpose = TRUE
)
## ArchR logging to : ArchRLogs/ArchR-plotMarkerHeatmap-cca71320e45e-Date-2020-11-24_Time-21-15-24.log
## If there is an issue, please report to github with logFile!
## Printing Top Marker Genes:
## C1_Inj:
##  Gm17644, Prss39, Lyg1, Nms, Il1rl1, Slc9a4, Tmem182, Vwc2l, Cxcr2, Ngef, Ugt1a5, Dnajb3, Ugt1a1, Serpinb2, Serpinb10, Il24, Il19, Ifi204, Ifi205, Olfr432
## C2_Hybrid:
##  Dnah7b, Crygf, Fn1, Pax3, Serpinb13, Serpinb3c, Serpinb7, C4bp-ps1, Pigr, Chil1, F5, Gm16548, Olfml2b, Tstd1, Mir194-1, Mir215, 1700007P06Rik, Il22ra2, Rspo3, Gm12070
## C3_UI:
##  Gm8580, Gm4792, Ikzf4, Irf1, Krtap9-5, Tmem235, Fscn2, Mrs2, Mss51, Wdfy4, Lrrc18, Mir5113, Gm5416, 2010005H15Rik, Mir5107, Sec31b, 1700080N15Rik, Gbp7, BC039966, Samd11
## Identified 504 markers!
## Adding Annotations..
## ArchR logging successful to : ArchRLogs/ArchR-plotMarkerHeatmap-cca71320e45e-Date-2020-11-24_Time-21-15-24.log
heatmapHBC <- plotMarkerHeatmap(
  seMarker = markerHBCCl, 
  cutOff = "FDR <= 0.01 & Log2FC >= 1.25", 
  transpose = TRUE
)
## ArchR logging to : ArchRLogs/ArchR-plotMarkerHeatmap-cca75470e121-Date-2020-11-24_Time-21-15-24.log
## If there is an issue, please report to github with logFile!
## Printing Top Marker Genes:
## C1_Inj:
##  Gm17644, Prss39, Lyg1, Nms, Il1rl1, Slc9a4, Tmem182, Vwc2l, Cxcr2, Ngef, Ugt1a5, Dnajb3, Ugt1a1, Serpinb2, Serpinb10, Il24, Il19, Ifi204, Ifi205, Olfr432
## C2_Hybrid:
##  Dnah7b, Crygf, Fn1, Pax3, Serpinb13, Serpinb3c, Serpinb7, C4bp-ps1, Pigr, Chil1, F5, Gm16548, Olfml2b, Tstd1, Mir194-1, Mir215, 1700007P06Rik, Il22ra2, Rspo3, Gm12070
## C3_UI:
##  Gm8580, Gm4792, Ikzf4, Irf1, Krtap9-5, Tmem235, Fscn2, Mrs2, Mss51, Wdfy4, Lrrc18, Mir5113, Gm5416, 2010005H15Rik, Mir5107, Sec31b, 1700080N15Rik, Gbp7, BC039966, Samd11
## Identified 504 markers!
## Preparing Main Heatmap..
## ArchR logging successful to : ArchRLogs/ArchR-plotMarkerHeatmap-cca75470e121-Date-2020-11-24_Time-21-15-24.log
ComplexHeatmap::draw(heatmapHBC, heatmap_legend_side = "bot", annotation_legend_side = "bot")

Plot for paper on preliminary HBC analysis

library(ggplot2)
umapDimsHBC <- ArchR::getEmbedding(proj, "UMAP_cor")
colnames(umapDimsHBC) <- c("UMAP1", "UMAP2")
umapDimsHBC$clHBCMerged <- getCellColData(proj, select = "clHBCMerged")$clHBCMerged
umapDimsHBC$treat <- getCellColData(proj, select = "treat")$treat

# cell state
pstate <- ggplot(umapDimsHBC, aes(x=UMAP1, y=UMAP2, color=clHBCMerged)) +
  geom_point(size = 1) + 
  theme_classic() +
  labs(color = "Cell state")

# injury treatment
pinj <- ggplot(umapDimsHBC, aes(x=UMAP1, y=UMAP2, color=treat)) +
  geom_point(size = 1) + 
  theme_classic() +
  labs(color = "Treatment") + 
  scale_color_manual(values = c("orange", "darkseagreen3")) 

cowplot::plot_grid(pstate, pinj, nrow=1)

ggsave("../plots/hbcDR.png", width=10)
## Saving 10 x 5 in image

Export gene activity data for custom downstream analysis

useMatrix="GeneScoreMatrix"
ArrowFiles <- getArrowFiles(proj)
featureDF <- ArchR:::.getFeatureDF(head(ArrowFiles, 2), "GeneScoreMatrix")
geneMat <- ArchR:::.getPartialMatrix(ArrowFiles, 
            featureDF = featureDF, threads = 1, useMatrix = "GeneScoreMatrix", 
            cellNames = rownames(proj@cellColData), progress = FALSE)
rownames(geneMat) <- featureDF$name
saveRDS(geneMat, file="../data/scATAC/geneMatArchrHbc.rds")

Create pseudobulk for peak calling

## ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-cca7d2932a6-Date-2020-11-24_Time-21-15-29.log
## If there is an issue, please report to github with logFile!
## C1_Inj (1 of 3) : CellGroups N = 4
## C2_Hybrid (2 of 3) : CellGroups N = 6
## C3_UI (3 of 3) : CellGroups N = 5
## 2020-11-24 21:15:30 : Creating Coverage Files!, 0.007 mins elapsed.
## 2020-11-24 21:15:30 : Batch Execution w/ safelapply!, 0.007 mins elapsed.
## 2020-11-24 21:15:30 : Group C1_Inj._.s1Inj (1 of 15) : Creating Group Coverage File : C1_Inj._.s1Inj.insertions.coverage.h5, 0.008 mins elapsed.
## Number of Cells = 500
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:15:51 : Group C1_Inj._.s2Inj (2 of 15) : Creating Group Coverage File : C1_Inj._.s2Inj.insertions.coverage.h5, 0.364 mins elapsed.
## Number of Cells = 263
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:16:11 : Group C1_Inj._.s3Inj (3 of 15) : Creating Group Coverage File : C1_Inj._.s3Inj.insertions.coverage.h5, 0.701 mins elapsed.
## Number of Cells = 164
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:16:32 : Group C1_Inj._.Other (4 of 15) : Creating Group Coverage File : C1_Inj._.Other.insertions.coverage.h5, 1.038 mins elapsed.
## Number of Cells = 54
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:16:58 : Group C2_Hybrid._.s3UI (5 of 15) : Creating Group Coverage File : C2_Hybrid._.s3UI.insertions.coverage.h5, 1.485 mins elapsed.
## Number of Cells = 377
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:17:44 : Group C2_Hybrid._.s3Inj (6 of 15) : Creating Group Coverage File : C2_Hybrid._.s3Inj.insertions.coverage.h5, 2.236 mins elapsed.
## Number of Cells = 346
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:18:17 : Group C2_Hybrid._.s1Inj (7 of 15) : Creating Group Coverage File : C2_Hybrid._.s1Inj.insertions.coverage.h5, 2.789 mins elapsed.
## Number of Cells = 287
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:18:40 : Group C2_Hybrid._.s2UI (8 of 15) : Creating Group Coverage File : C2_Hybrid._.s2UI.insertions.coverage.h5, 3.175 mins elapsed.
## Number of Cells = 160
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:18:59 : Group C2_Hybrid._.s2Inj (9 of 15) : Creating Group Coverage File : C2_Hybrid._.s2Inj.insertions.coverage.h5, 3.492 mins elapsed.
## Number of Cells = 93
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:19:16 : Group C2_Hybrid._.s1UI (10 of 15) : Creating Group Coverage File : C2_Hybrid._.s1UI.insertions.coverage.h5, 3.785 mins elapsed.
## Number of Cells = 87
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:19:33 : Group C3_UI._.s2UI (11 of 15) : Creating Group Coverage File : C3_UI._.s2UI.insertions.coverage.h5, 4.061 mins elapsed.
## Number of Cells = 500
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:19:54 : Group C3_UI._.s1UI (12 of 15) : Creating Group Coverage File : C3_UI._.s1UI.insertions.coverage.h5, 4.415 mins elapsed.
## Number of Cells = 355
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:20:13 : Group C3_UI._.s3UI (13 of 15) : Creating Group Coverage File : C3_UI._.s3UI.insertions.coverage.h5, 4.735 mins elapsed.
## Number of Cells = 178
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:20:30 : Group C3_UI._.s3Inj (14 of 15) : Creating Group Coverage File : C3_UI._.s3Inj.insertions.coverage.h5, 5.009 mins elapsed.
## Number of Cells = 55
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:20:45 : Group C3_UI._.Other (15 of 15) : Creating Group Coverage File : C3_UI._.Other.insertions.coverage.h5, 5.262 mins elapsed.
## Number of Cells = 51
## Coverage File Exists!
## Added Coverage Group
## Added Metadata Group
## Added ArrowCoverage Class
## Added Coverage/Info
## Added Coverage/Info/CellNames
## 2020-11-24 21:21:02 : Adding Kmer Bias to Coverage Files!, 5.546 mins elapsed.
## Kmer Bias chr1 (1 of 21)
## chr1 Coverage File chr1 (1 of 15)
## Coverage File chr1 (2 of 15)
## Coverage File chr1 (3 of 15)
## Coverage File chr1 (4 of 15)
## Coverage File chr1 (5 of 15)
## Coverage File chr1 (6 of 15)
## Coverage File chr1 (7 of 15)
## Coverage File chr1 (8 of 15)
## Coverage File chr1 (9 of 15)
## Coverage File chr1 (10 of 15)
## Coverage File chr1 (11 of 15)
## Coverage File chr1 (12 of 15)
## Coverage File chr1 (13 of 15)
## Coverage File chr1 (14 of 15)
## Coverage File chr1 (15 of 15)
## Kmer Bias chr10 (2 of 21)
## chr10 Coverage File chr10 (1 of 15)
## Coverage File chr10 (2 of 15)
## Coverage File chr10 (3 of 15)
## Coverage File chr10 (4 of 15)
## Coverage File chr10 (5 of 15)
## Coverage File chr10 (6 of 15)
## Coverage File chr10 (7 of 15)
## Coverage File chr10 (8 of 15)
## Coverage File chr10 (9 of 15)
## Coverage File chr10 (10 of 15)
## Coverage File chr10 (11 of 15)
## Coverage File chr10 (12 of 15)
## Coverage File chr10 (13 of 15)
## Coverage File chr10 (14 of 15)
## Coverage File chr10 (15 of 15)
## Kmer Bias chr11 (3 of 21)
## chr11 Coverage File chr11 (1 of 15)
## Coverage File chr11 (2 of 15)
## Coverage File chr11 (3 of 15)
## Coverage File chr11 (4 of 15)
## Coverage File chr11 (5 of 15)
## Coverage File chr11 (6 of 15)
## Coverage File chr11 (7 of 15)
## Coverage File chr11 (8 of 15)
## Coverage File chr11 (9 of 15)
## Coverage File chr11 (10 of 15)
## Coverage File chr11 (11 of 15)
## Coverage File chr11 (12 of 15)
## Coverage File chr11 (13 of 15)
## Coverage File chr11 (14 of 15)
## Coverage File chr11 (15 of 15)
## Kmer Bias chr12 (4 of 21)
## chr12 Coverage File chr12 (1 of 15)
## Coverage File chr12 (2 of 15)
## Coverage File chr12 (3 of 15)
## Coverage File chr12 (4 of 15)
## Coverage File chr12 (5 of 15)
## Coverage File chr12 (6 of 15)
## Coverage File chr12 (7 of 15)
## Coverage File chr12 (8 of 15)
## Coverage File chr12 (9 of 15)
## Coverage File chr12 (10 of 15)
## Coverage File chr12 (11 of 15)
## Coverage File chr12 (12 of 15)
## Coverage File chr12 (13 of 15)
## Coverage File chr12 (14 of 15)
## Coverage File chr12 (15 of 15)
## Kmer Bias chr13 (5 of 21)
## chr13 Coverage File chr13 (1 of 15)
## Coverage File chr13 (2 of 15)
## Coverage File chr13 (3 of 15)
## Coverage File chr13 (4 of 15)
## Coverage File chr13 (5 of 15)
## Coverage File chr13 (6 of 15)
## Coverage File chr13 (7 of 15)
## Coverage File chr13 (8 of 15)
## Coverage File chr13 (9 of 15)
## Coverage File chr13 (10 of 15)
## Coverage File chr13 (11 of 15)
## Coverage File chr13 (12 of 15)
## Coverage File chr13 (13 of 15)
## Coverage File chr13 (14 of 15)
## Coverage File chr13 (15 of 15)
## Kmer Bias chr14 (6 of 21)
## chr14 Coverage File chr14 (1 of 15)
## Coverage File chr14 (2 of 15)
## Coverage File chr14 (3 of 15)
## Coverage File chr14 (4 of 15)
## Coverage File chr14 (5 of 15)
## Coverage File chr14 (6 of 15)
## Coverage File chr14 (7 of 15)
## Coverage File chr14 (8 of 15)
## Coverage File chr14 (9 of 15)
## Coverage File chr14 (10 of 15)
## Coverage File chr14 (11 of 15)
## Coverage File chr14 (12 of 15)
## Coverage File chr14 (13 of 15)
## Coverage File chr14 (14 of 15)
## Coverage File chr14 (15 of 15)
## Kmer Bias chr15 (7 of 21)
## chr15 Coverage File chr15 (1 of 15)
## Coverage File chr15 (2 of 15)
## Coverage File chr15 (3 of 15)
## Coverage File chr15 (4 of 15)
## Coverage File chr15 (5 of 15)
## Coverage File chr15 (6 of 15)
## Coverage File chr15 (7 of 15)
## Coverage File chr15 (8 of 15)
## Coverage File chr15 (9 of 15)
## Coverage File chr15 (10 of 15)
## Coverage File chr15 (11 of 15)
## Coverage File chr15 (12 of 15)
## Coverage File chr15 (13 of 15)
## Coverage File chr15 (14 of 15)
## Coverage File chr15 (15 of 15)
## Kmer Bias chr16 (8 of 21)
## chr16 Coverage File chr16 (1 of 15)
## Coverage File chr16 (2 of 15)
## Coverage File chr16 (3 of 15)
## Coverage File chr16 (4 of 15)
## Coverage File chr16 (5 of 15)
## Coverage File chr16 (6 of 15)
## Coverage File chr16 (7 of 15)
## Coverage File chr16 (8 of 15)
## Coverage File chr16 (9 of 15)
## Coverage File chr16 (10 of 15)
## Coverage File chr16 (11 of 15)
## Coverage File chr16 (12 of 15)
## Coverage File chr16 (13 of 15)
## Coverage File chr16 (14 of 15)
## Coverage File chr16 (15 of 15)
## Kmer Bias chr17 (9 of 21)
## chr17 Coverage File chr17 (1 of 15)
## Coverage File chr17 (2 of 15)
## Coverage File chr17 (3 of 15)
## Coverage File chr17 (4 of 15)
## Coverage File chr17 (5 of 15)
## Coverage File chr17 (6 of 15)
## Coverage File chr17 (7 of 15)
## Coverage File chr17 (8 of 15)
## Coverage File chr17 (9 of 15)
## Coverage File chr17 (10 of 15)
## Coverage File chr17 (11 of 15)
## Coverage File chr17 (12 of 15)
## Coverage File chr17 (13 of 15)
## Coverage File chr17 (14 of 15)
## Coverage File chr17 (15 of 15)
## Kmer Bias chr18 (10 of 21)
## chr18 Coverage File chr18 (1 of 15)
## Coverage File chr18 (2 of 15)
## Coverage File chr18 (3 of 15)
## Coverage File chr18 (4 of 15)
## Coverage File chr18 (5 of 15)
## Coverage File chr18 (6 of 15)
## Coverage File chr18 (7 of 15)
## Coverage File chr18 (8 of 15)
## Coverage File chr18 (9 of 15)
## Coverage File chr18 (10 of 15)
## Coverage File chr18 (11 of 15)
## Coverage File chr18 (12 of 15)
## Coverage File chr18 (13 of 15)
## Coverage File chr18 (14 of 15)
## Coverage File chr18 (15 of 15)
## Kmer Bias chr19 (11 of 21)
## chr19 Coverage File chr19 (1 of 15)
## Coverage File chr19 (2 of 15)
## Coverage File chr19 (3 of 15)
## Coverage File chr19 (4 of 15)
## Coverage File chr19 (5 of 15)
## Coverage File chr19 (6 of 15)
## Coverage File chr19 (7 of 15)
## Coverage File chr19 (8 of 15)
## Coverage File chr19 (9 of 15)
## Coverage File chr19 (10 of 15)
## Coverage File chr19 (11 of 15)
## Coverage File chr19 (12 of 15)
## Coverage File chr19 (13 of 15)
## Coverage File chr19 (14 of 15)
## Coverage File chr19 (15 of 15)
## Kmer Bias chr2 (12 of 21)
## chr2 Coverage File chr2 (1 of 15)
## Coverage File chr2 (2 of 15)
## Coverage File chr2 (3 of 15)
## Coverage File chr2 (4 of 15)
## Coverage File chr2 (5 of 15)
## Coverage File chr2 (6 of 15)
## Coverage File chr2 (7 of 15)
## Coverage File chr2 (8 of 15)
## Coverage File chr2 (9 of 15)
## Coverage File chr2 (10 of 15)
## Coverage File chr2 (11 of 15)
## Coverage File chr2 (12 of 15)
## Coverage File chr2 (13 of 15)
## Coverage File chr2 (14 of 15)
## Coverage File chr2 (15 of 15)
## Kmer Bias chr3 (13 of 21)
## chr3 Coverage File chr3 (1 of 15)
## Coverage File chr3 (2 of 15)
## Coverage File chr3 (3 of 15)
## Coverage File chr3 (4 of 15)
## Coverage File chr3 (5 of 15)
## Coverage File chr3 (6 of 15)
## Coverage File chr3 (7 of 15)
## Coverage File chr3 (8 of 15)
## Coverage File chr3 (9 of 15)
## Coverage File chr3 (10 of 15)
## Coverage File chr3 (11 of 15)
## Coverage File chr3 (12 of 15)
## Coverage File chr3 (13 of 15)
## Coverage File chr3 (14 of 15)
## Coverage File chr3 (15 of 15)
## Kmer Bias chr4 (14 of 21)
## chr4 Coverage File chr4 (1 of 15)
## Coverage File chr4 (2 of 15)
## Coverage File chr4 (3 of 15)
## Coverage File chr4 (4 of 15)
## Coverage File chr4 (5 of 15)
## Coverage File chr4 (6 of 15)
## Coverage File chr4 (7 of 15)
## Coverage File chr4 (8 of 15)
## Coverage File chr4 (9 of 15)
## Coverage File chr4 (10 of 15)
## Coverage File chr4 (11 of 15)
## Coverage File chr4 (12 of 15)
## Coverage File chr4 (13 of 15)
## Coverage File chr4 (14 of 15)
## Coverage File chr4 (15 of 15)
## Kmer Bias chr5 (15 of 21)
## chr5 Coverage File chr5 (1 of 15)
## Coverage File chr5 (2 of 15)
## Coverage File chr5 (3 of 15)
## Coverage File chr5 (4 of 15)
## Coverage File chr5 (5 of 15)
## Coverage File chr5 (6 of 15)
## Coverage File chr5 (7 of 15)
## Coverage File chr5 (8 of 15)
## Coverage File chr5 (9 of 15)
## Coverage File chr5 (10 of 15)
## Coverage File chr5 (11 of 15)
## Coverage File chr5 (12 of 15)
## Coverage File chr5 (13 of 15)
## Coverage File chr5 (14 of 15)
## Coverage File chr5 (15 of 15)
## Kmer Bias chr6 (16 of 21)
## chr6 Coverage File chr6 (1 of 15)
## Coverage File chr6 (2 of 15)
## Coverage File chr6 (3 of 15)
## Coverage File chr6 (4 of 15)
## Coverage File chr6 (5 of 15)
## Coverage File chr6 (6 of 15)
## Coverage File chr6 (7 of 15)
## Coverage File chr6 (8 of 15)
## Coverage File chr6 (9 of 15)
## Coverage File chr6 (10 of 15)
## Coverage File chr6 (11 of 15)
## Coverage File chr6 (12 of 15)
## Coverage File chr6 (13 of 15)
## Coverage File chr6 (14 of 15)
## Coverage File chr6 (15 of 15)
## Kmer Bias chr7 (17 of 21)
## chr7 Coverage File chr7 (1 of 15)
## Coverage File chr7 (2 of 15)
## Coverage File chr7 (3 of 15)
## Coverage File chr7 (4 of 15)
## Coverage File chr7 (5 of 15)
## Coverage File chr7 (6 of 15)
## Coverage File chr7 (7 of 15)
## Coverage File chr7 (8 of 15)
## Coverage File chr7 (9 of 15)
## Coverage File chr7 (10 of 15)
## Coverage File chr7 (11 of 15)
## Coverage File chr7 (12 of 15)
## Coverage File chr7 (13 of 15)
## Coverage File chr7 (14 of 15)
## Coverage File chr7 (15 of 15)
## Kmer Bias chr8 (18 of 21)
## chr8 Coverage File chr8 (1 of 15)
## Coverage File chr8 (2 of 15)
## Coverage File chr8 (3 of 15)
## Coverage File chr8 (4 of 15)
## Coverage File chr8 (5 of 15)
## Coverage File chr8 (6 of 15)
## Coverage File chr8 (7 of 15)
## Coverage File chr8 (8 of 15)
## Coverage File chr8 (9 of 15)
## Coverage File chr8 (10 of 15)
## Coverage File chr8 (11 of 15)
## Coverage File chr8 (12 of 15)
## Coverage File chr8 (13 of 15)
## Coverage File chr8 (14 of 15)
## Coverage File chr8 (15 of 15)
## Kmer Bias chr9 (19 of 21)
## chr9 Coverage File chr9 (1 of 15)
## Coverage File chr9 (2 of 15)
## Coverage File chr9 (3 of 15)
## Coverage File chr9 (4 of 15)
## Coverage File chr9 (5 of 15)
## Coverage File chr9 (6 of 15)
## Coverage File chr9 (7 of 15)
## Coverage File chr9 (8 of 15)
## Coverage File chr9 (9 of 15)
## Coverage File chr9 (10 of 15)
## Coverage File chr9 (11 of 15)
## Coverage File chr9 (12 of 15)
## Coverage File chr9 (13 of 15)
## Coverage File chr9 (14 of 15)
## Coverage File chr9 (15 of 15)
## Kmer Bias chrX (20 of 21)
## chrX Coverage File chrX (1 of 15)
## Coverage File chrX (2 of 15)
## Coverage File chrX (3 of 15)
## Coverage File chrX (4 of 15)
## Coverage File chrX (5 of 15)
## Coverage File chrX (6 of 15)
## Coverage File chrX (7 of 15)
## Coverage File chrX (8 of 15)
## Coverage File chrX (9 of 15)
## Coverage File chrX (10 of 15)
## Coverage File chrX (11 of 15)
## Coverage File chrX (12 of 15)
## Coverage File chrX (13 of 15)
## Coverage File chrX (14 of 15)
## Coverage File chrX (15 of 15)
## Kmer Bias chrY (21 of 21)
## chrY Coverage File chrY (1 of 15)
## Coverage File chrY (2 of 15)
## Coverage File chrY (3 of 15)
## Coverage File chrY (4 of 15)
## Coverage File chrY (5 of 15)
## Coverage File chrY (6 of 15)
## Coverage File chrY (7 of 15)
## Coverage File chrY (8 of 15)
## Coverage File chrY (9 of 15)
## Coverage File chrY (10 of 15)
## Coverage File chrY (11 of 15)
## Coverage File chrY (12 of 15)
## Coverage File chrY (13 of 15)
## Coverage File chrY (14 of 15)
## Coverage File chrY (15 of 15)
## Completed Kmer Bias Calculation
## Adding Kmer Bias (1 of 15)
## Adding Kmer Bias (2 of 15)
## Adding Kmer Bias (3 of 15)
## Adding Kmer Bias (4 of 15)
## Adding Kmer Bias (5 of 15)
## Adding Kmer Bias (6 of 15)
## Adding Kmer Bias (7 of 15)
## Adding Kmer Bias (8 of 15)
## Adding Kmer Bias (9 of 15)
## Adding Kmer Bias (10 of 15)
## Adding Kmer Bias (11 of 15)
## Adding Kmer Bias (12 of 15)
## Adding Kmer Bias (13 of 15)
## Adding Kmer Bias (14 of 15)
## Adding Kmer Bias (15 of 15)
## 2020-11-24 21:25:48 : Finished Creation of Coverage Files!, 10.317 mins elapsed.
## ArchR logging successful to : ArchRLogs/ArchR-addGroupCoverages-cca7d2932a6-Date-2020-11-24_Time-21-15-29.log

Peak calling

## ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-cca771c1778a-Date-2020-11-24_Time-21-25-49.log
## If there is an issue, please report to github with logFile!
## Calling Peaks with Macs2
## 2020-11-24 21:25:49 : Peak Calling Parameters!, 0.003 mins elapsed.
##               Group nCells nCellsUsed nReplicates nMin nMax maxPeaks
## C1_Inj       C1_Inj   1486        981           4   54  500   150000
## C2_Hybrid C2_Hybrid   1350       1350           6   87  377   150000
## C3_UI         C3_UI   1240       1139           5   51  500   150000
## 2020-11-24 21:25:49 : Batching Peak Calls!, 0.003 mins elapsed.
## 2020-11-24 21:25:49 : Batch Execution w/ safelapply!, 0 mins elapsed.
## 2020-11-24 21:25:49 : Group 1 of 15, Calling Peaks with MACS2!, 0 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C1_Inj._.s1Inj-1 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C1_Inj._.s1Inj-1.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:27:43 : Group 2 of 15, Calling Peaks with MACS2!, 1.903 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C1_Inj._.s2Inj-2 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C1_Inj._.s2Inj-2.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:29:24 : Group 3 of 15, Calling Peaks with MACS2!, 3.574 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C1_Inj._.s3Inj-3 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C1_Inj._.s3Inj-3.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:30:55 : Group 4 of 15, Calling Peaks with MACS2!, 5.105 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C1_Inj._.Other-4 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C1_Inj._.Other-4.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:31:55 : Group 5 of 15, Calling Peaks with MACS2!, 6.091 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C2_Hybrid._.s3UI-5 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C2_Hybrid._.s3UI-5.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:34:07 : Group 6 of 15, Calling Peaks with MACS2!, 8.296 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C2_Hybrid._.s3Inj-6 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C2_Hybrid._.s3Inj-6.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:35:58 : Group 7 of 15, Calling Peaks with MACS2!, 10.156 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C2_Hybrid._.s1Inj-7 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C2_Hybrid._.s1Inj-7.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:37:22 : Group 8 of 15, Calling Peaks with MACS2!, 11.542 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C2_Hybrid._.s2UI-8 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C2_Hybrid._.s2UI-8.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:38:20 : Group 9 of 15, Calling Peaks with MACS2!, 12.515 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C2_Hybrid._.s2Inj-9 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C2_Hybrid._.s2Inj-9.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:39:30 : Group 10 of 15, Calling Peaks with MACS2!, 13.683 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C2_Hybrid._.s1UI-10 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C2_Hybrid._.s1UI-10.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:40:15 : Group 11 of 15, Calling Peaks with MACS2!, 14.434 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C3_UI._.s2UI-11 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C3_UI._.s2UI-11.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:41:57 : Group 12 of 15, Calling Peaks with MACS2!, 16.125 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C3_UI._.s1UI-12 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C3_UI._.s1UI-12.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:43:24 : Group 13 of 15, Calling Peaks with MACS2!, 17.581 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C3_UI._.s3UI-13 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C3_UI._.s3UI-13.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:44:38 : Group 14 of 15, Calling Peaks with MACS2!, 18.809 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C3_UI._.s3Inj-14 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C3_UI._.s3Inj-14.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:45:22 : Group 15 of 15, Calling Peaks with MACS2!, 19.548 mins elapsed.
## Running Macs2 with Params : macs2 callpeak -g 1.87e+09 --name C3_UI._.Other-15 --treatment /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds/C3_UI._.Other-15.insertions.bed --outdir /Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/InsertionBeds --format BED --call-summits --keep-dup all --nomodel --nolambda --shift -75 --extsize 150 -q 0.1
## 2020-11-24 21:45:59 : Identifying Reproducible Peaks!, 20.176 mins elapsed.
## Annotating Peaks : Nearest Gene
## Annotating Peaks : Gene
## Annotating Peaks : TSS
## Annotating Peaks : GC
## [1] "/Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/C1_Inj-reproduciblePeaks.gr.rds"
## Annotating Peaks : Nearest Gene
## Annotating Peaks : Gene
## Annotating Peaks : TSS
## Annotating Peaks : GC
## [1] "/Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/C2_Hybrid-reproduciblePeaks.gr.rds"
## Annotating Peaks : Nearest Gene
## Annotating Peaks : Gene
## Annotating Peaks : TSS
## Annotating Peaks : GC
## [1] "/Users/koenvandenberge/Dropbox/research/brainStat/hbcRegenGithub/data/scATAC/archR_samples_pairwise/PeakCalls/C3_UI-reproduciblePeaks.gr.rds"
## 2020-11-24 21:46:35 : Creating Union Peak Set!, 20.766 mins elapsed.
## Converged after 7 iterations!
## Plotting Ggplot!
## 2020-11-24 21:46:39 : Finished Creating Union Peak Set (183713)!, 20.827 mins elapsed.
## ArchR logging to : ArchRLogs/ArchR-addPeakMatrix-cca78895fb1-Date-2020-11-24_Time-21-46-39.log
## If there is an issue, please report to github with logFile!
## 2020-11-24 21:46:39 : Batch Execution w/ safelapply!, 0 mins elapsed.
## 2020-11-24 21:46:39 : Adding s1Inj to PeakMatrix for Chr (1 of 20)!, 0.009 mins elapsed.
## 2020-11-24 21:46:41 : Adding s1Inj to PeakMatrix for Chr (2 of 20)!, 0.044 mins elapsed.
## 2020-11-24 21:46:44 : Adding s1Inj to PeakMatrix for Chr (3 of 20)!, 0.081 mins elapsed.
## 2020-11-24 21:46:46 : Adding s1Inj to PeakMatrix for Chr (4 of 20)!, 0.114 mins elapsed.
## 2020-11-24 21:46:48 : Adding s1Inj to PeakMatrix for Chr (5 of 20)!, 0.149 mins elapsed.
## 2020-11-24 21:46:50 : Adding s1Inj to PeakMatrix for Chr (6 of 20)!, 0.183 mins elapsed.
## 2020-11-24 21:46:52 : Adding s1Inj to PeakMatrix for Chr (7 of 20)!, 0.216 mins elapsed.
## 2020-11-24 21:46:54 : Adding s1Inj to PeakMatrix for Chr (8 of 20)!, 0.252 mins elapsed.
## 2020-11-24 21:46:56 : Adding s1Inj to PeakMatrix for Chr (9 of 20)!, 0.286 mins elapsed.
## 2020-11-24 21:46:58 : Adding s1Inj to PeakMatrix for Chr (10 of 20)!, 0.32 mins elapsed.
## 2020-11-24 21:47:00 : Adding s1Inj to PeakMatrix for Chr (11 of 20)!, 0.353 mins elapsed.
## 2020-11-24 21:47:02 : Adding s1Inj to PeakMatrix for Chr (12 of 20)!, 0.391 mins elapsed.
## 2020-11-24 21:47:04 : Adding s1Inj to PeakMatrix for Chr (13 of 20)!, 0.423 mins elapsed.
## 2020-11-24 21:47:06 : Adding s1Inj to PeakMatrix for Chr (14 of 20)!, 0.454 mins elapsed.
## 2020-11-24 21:47:08 : Adding s1Inj to PeakMatrix for Chr (15 of 20)!, 0.484 mins elapsed.
## 2020-11-24 21:47:10 : Adding s1Inj to PeakMatrix for Chr (16 of 20)!, 0.516 mins elapsed.
## 2020-11-24 21:47:11 : Adding s1Inj to PeakMatrix for Chr (17 of 20)!, 0.544 mins elapsed.
## 2020-11-24 21:47:13 : Adding s1Inj to PeakMatrix for Chr (18 of 20)!, 0.576 mins elapsed.
## 2020-11-24 21:47:15 : Adding s1Inj to PeakMatrix for Chr (19 of 20)!, 0.604 mins elapsed.
## 2020-11-24 21:47:17 : Adding s1Inj to PeakMatrix for Chr (20 of 20)!, 0.63 mins elapsed.
## 2020-11-24 21:47:19 : Adding s3Inj to PeakMatrix for Chr (1 of 20)!, 0.01 mins elapsed.
## 2020-11-24 21:47:21 : Adding s3Inj to PeakMatrix for Chr (2 of 20)!, 0.041 mins elapsed.
## 2020-11-24 21:47:23 : Adding s3Inj to PeakMatrix for Chr (3 of 20)!, 0.074 mins elapsed.
## 2020-11-24 21:47:25 : Adding s3Inj to PeakMatrix for Chr (4 of 20)!, 0.107 mins elapsed.
## 2020-11-24 21:47:27 : Adding s3Inj to PeakMatrix for Chr (5 of 20)!, 0.145 mins elapsed.
## 2020-11-24 21:47:29 : Adding s3Inj to PeakMatrix for Chr (6 of 20)!, 0.186 mins elapsed.
## 2020-11-24 21:47:32 : Adding s3Inj to PeakMatrix for Chr (7 of 20)!, 0.227 mins elapsed.
## 2020-11-24 21:47:34 : Adding s3Inj to PeakMatrix for Chr (8 of 20)!, 0.27 mins elapsed.
## 2020-11-24 21:47:37 : Adding s3Inj to PeakMatrix for Chr (9 of 20)!, 0.309 mins elapsed.
## 2020-11-24 21:47:39 : Adding s3Inj to PeakMatrix for Chr (10 of 20)!, 0.343 mins elapsed.
## 2020-11-24 21:47:41 : Adding s3Inj to PeakMatrix for Chr (11 of 20)!, 0.375 mins elapsed.
## 2020-11-24 21:47:43 : Adding s3Inj to PeakMatrix for Chr (12 of 20)!, 0.406 mins elapsed.
## 2020-11-24 21:47:44 : Adding s3Inj to PeakMatrix for Chr (13 of 20)!, 0.432 mins elapsed.
## 2020-11-24 21:47:46 : Adding s3Inj to PeakMatrix for Chr (14 of 20)!, 0.458 mins elapsed.
## 2020-11-24 21:47:47 : Adding s3Inj to PeakMatrix for Chr (15 of 20)!, 0.483 mins elapsed.
## 2020-11-24 21:47:49 : Adding s3Inj to PeakMatrix for Chr (16 of 20)!, 0.509 mins elapsed.
## 2020-11-24 21:47:50 : Adding s3Inj to PeakMatrix for Chr (17 of 20)!, 0.533 mins elapsed.
## 2020-11-24 21:47:52 : Adding s3Inj to PeakMatrix for Chr (18 of 20)!, 0.559 mins elapsed.
## 2020-11-24 21:47:53 : Adding s3Inj to PeakMatrix for Chr (19 of 20)!, 0.582 mins elapsed.
## 2020-11-24 21:47:55 : Adding s3Inj to PeakMatrix for Chr (20 of 20)!, 0.605 mins elapsed.
## 2020-11-24 21:47:57 : Adding s3UI to PeakMatrix for Chr (1 of 20)!, 0.009 mins elapsed.
## 2020-11-24 21:47:58 : Adding s3UI to PeakMatrix for Chr (2 of 20)!, 0.038 mins elapsed.
## 2020-11-24 21:48:00 : Adding s3UI to PeakMatrix for Chr (3 of 20)!, 0.068 mins elapsed.
## 2020-11-24 21:48:02 : Adding s3UI to PeakMatrix for Chr (4 of 20)!, 0.095 mins elapsed.
## 2020-11-24 21:48:03 : Adding s3UI to PeakMatrix for Chr (5 of 20)!, 0.124 mins elapsed.
## 2020-11-24 21:48:05 : Adding s3UI to PeakMatrix for Chr (6 of 20)!, 0.153 mins elapsed.
## 2020-11-24 21:48:07 : Adding s3UI to PeakMatrix for Chr (7 of 20)!, 0.18 mins elapsed.
## 2020-11-24 21:48:09 : Adding s3UI to PeakMatrix for Chr (8 of 20)!, 0.21 mins elapsed.
## 2020-11-24 21:48:10 : Adding s3UI to PeakMatrix for Chr (9 of 20)!, 0.239 mins elapsed.
## 2020-11-24 21:48:12 : Adding s3UI to PeakMatrix for Chr (10 of 20)!, 0.267 mins elapsed.
## 2020-11-24 21:48:14 : Adding s3UI to PeakMatrix for Chr (11 of 20)!, 0.295 mins elapsed.
## 2020-11-24 21:48:15 : Adding s3UI to PeakMatrix for Chr (12 of 20)!, 0.325 mins elapsed.
## 2020-11-24 21:48:17 : Adding s3UI to PeakMatrix for Chr (13 of 20)!, 0.353 mins elapsed.
## 2020-11-24 21:48:19 : Adding s3UI to PeakMatrix for Chr (14 of 20)!, 0.379 mins elapsed.
## 2020-11-24 21:48:20 : Adding s3UI to PeakMatrix for Chr (15 of 20)!, 0.405 mins elapsed.
## 2020-11-24 21:48:22 : Adding s3UI to PeakMatrix for Chr (16 of 20)!, 0.431 mins elapsed.
## 2020-11-24 21:48:23 : Adding s3UI to PeakMatrix for Chr (17 of 20)!, 0.455 mins elapsed.
## 2020-11-24 21:48:25 : Adding s3UI to PeakMatrix for Chr (18 of 20)!, 0.481 mins elapsed.
## 2020-11-24 21:48:26 : Adding s3UI to PeakMatrix for Chr (19 of 20)!, 0.505 mins elapsed.
## 2020-11-24 21:48:28 : Adding s3UI to PeakMatrix for Chr (20 of 20)!, 0.529 mins elapsed.
## 2020-11-24 21:48:30 : Adding s2UI to PeakMatrix for Chr (1 of 20)!, 0.009 mins elapsed.
## 2020-11-24 21:48:31 : Adding s2UI to PeakMatrix for Chr (2 of 20)!, 0.036 mins elapsed.
## 2020-11-24 21:48:33 : Adding s2UI to PeakMatrix for Chr (3 of 20)!, 0.063 mins elapsed.
## 2020-11-24 21:48:34 : Adding s2UI to PeakMatrix for Chr (4 of 20)!, 0.089 mins elapsed.
## 2020-11-24 21:48:36 : Adding s2UI to PeakMatrix for Chr (5 of 20)!, 0.116 mins elapsed.
## 2020-11-24 21:48:38 : Adding s2UI to PeakMatrix for Chr (6 of 20)!, 0.142 mins elapsed.
## 2020-11-24 21:48:39 : Adding s2UI to PeakMatrix for Chr (7 of 20)!, 0.167 mins elapsed.
## 2020-11-24 21:48:41 : Adding s2UI to PeakMatrix for Chr (8 of 20)!, 0.194 mins elapsed.
## 2020-11-24 21:48:42 : Adding s2UI to PeakMatrix for Chr (9 of 20)!, 0.22 mins elapsed.
## 2020-11-24 21:48:44 : Adding s2UI to PeakMatrix for Chr (10 of 20)!, 0.245 mins elapsed.
## 2020-11-24 21:48:45 : Adding s2UI to PeakMatrix for Chr (11 of 20)!, 0.271 mins elapsed.
## 2020-11-24 21:48:47 : Adding s2UI to PeakMatrix for Chr (12 of 20)!, 0.298 mins elapsed.
## 2020-11-24 21:48:48 : Adding s2UI to PeakMatrix for Chr (13 of 20)!, 0.323 mins elapsed.
## 2020-11-24 21:48:50 : Adding s2UI to PeakMatrix for Chr (14 of 20)!, 0.348 mins elapsed.
## 2020-11-24 21:48:51 : Adding s2UI to PeakMatrix for Chr (15 of 20)!, 0.374 mins elapsed.
## 2020-11-24 21:48:53 : Adding s2UI to PeakMatrix for Chr (16 of 20)!, 0.4 mins elapsed.
## 2020-11-24 21:48:55 : Adding s2UI to PeakMatrix for Chr (17 of 20)!, 0.426 mins elapsed.
## 2020-11-24 21:48:56 : Adding s2UI to PeakMatrix for Chr (18 of 20)!, 0.453 mins elapsed.
## 2020-11-24 21:48:58 : Adding s2UI to PeakMatrix for Chr (19 of 20)!, 0.477 mins elapsed.
## 2020-11-24 21:48:59 : Adding s2UI to PeakMatrix for Chr (20 of 20)!, 0.501 mins elapsed.
## 2020-11-24 21:49:01 : Adding s2Inj to PeakMatrix for Chr (1 of 20)!, 0.01 mins elapsed.
## 2020-11-24 21:49:03 : Adding s2Inj to PeakMatrix for Chr (2 of 20)!, 0.038 mins elapsed.
## 2020-11-24 21:49:04 : Adding s2Inj to PeakMatrix for Chr (3 of 20)!, 0.064 mins elapsed.
## 2020-11-24 21:49:06 : Adding s2Inj to PeakMatrix for Chr (4 of 20)!, 0.089 mins elapsed.
## 2020-11-24 21:49:08 : Adding s2Inj to PeakMatrix for Chr (5 of 20)!, 0.115 mins elapsed.
## 2020-11-24 21:49:09 : Adding s2Inj to PeakMatrix for Chr (6 of 20)!, 0.142 mins elapsed.
## 2020-11-24 21:49:11 : Adding s2Inj to PeakMatrix for Chr (7 of 20)!, 0.166 mins elapsed.
## 2020-11-24 21:49:12 : Adding s2Inj to PeakMatrix for Chr (8 of 20)!, 0.193 mins elapsed.
## 2020-11-24 21:49:14 : Adding s2Inj to PeakMatrix for Chr (9 of 20)!, 0.218 mins elapsed.
## 2020-11-24 21:49:15 : Adding s2Inj to PeakMatrix for Chr (10 of 20)!, 0.242 mins elapsed.
## 2020-11-24 21:49:17 : Adding s2Inj to PeakMatrix for Chr (11 of 20)!, 0.267 mins elapsed.
## 2020-11-24 21:49:18 : Adding s2Inj to PeakMatrix for Chr (12 of 20)!, 0.293 mins elapsed.
## 2020-11-24 21:49:20 : Adding s2Inj to PeakMatrix for Chr (13 of 20)!, 0.317 mins elapsed.
## 2020-11-24 21:49:21 : Adding s2Inj to PeakMatrix for Chr (14 of 20)!, 0.341 mins elapsed.
## 2020-11-24 21:49:23 : Adding s2Inj to PeakMatrix for Chr (15 of 20)!, 0.365 mins elapsed.
## 2020-11-24 21:49:24 : Adding s2Inj to PeakMatrix for Chr (16 of 20)!, 0.39 mins elapsed.
## 2020-11-24 21:49:25 : Adding s2Inj to PeakMatrix for Chr (17 of 20)!, 0.414 mins elapsed.
## 2020-11-24 21:49:27 : Adding s2Inj to PeakMatrix for Chr (18 of 20)!, 0.439 mins elapsed.
## 2020-11-24 21:49:28 : Adding s2Inj to PeakMatrix for Chr (19 of 20)!, 0.463 mins elapsed.
## 2020-11-24 21:49:30 : Adding s2Inj to PeakMatrix for Chr (20 of 20)!, 0.487 mins elapsed.
## 2020-11-24 21:49:32 : Adding s1UI to PeakMatrix for Chr (1 of 20)!, 0.011 mins elapsed.
## 2020-11-24 21:49:33 : Adding s1UI to PeakMatrix for Chr (2 of 20)!, 0.036 mins elapsed.
## 2020-11-24 21:49:35 : Adding s1UI to PeakMatrix for Chr (3 of 20)!, 0.062 mins elapsed.
## 2020-11-24 21:49:36 : Adding s1UI to PeakMatrix for Chr (4 of 20)!, 0.085 mins elapsed.
## 2020-11-24 21:49:38 : Adding s1UI to PeakMatrix for Chr (5 of 20)!, 0.11 mins elapsed.
## 2020-11-24 21:49:39 : Adding s1UI to PeakMatrix for Chr (6 of 20)!, 0.134 mins elapsed.
## 2020-11-24 21:49:41 : Adding s1UI to PeakMatrix for Chr (7 of 20)!, 0.157 mins elapsed.
## 2020-11-24 21:49:42 : Adding s1UI to PeakMatrix for Chr (8 of 20)!, 0.182 mins elapsed.
## 2020-11-24 21:49:44 : Adding s1UI to PeakMatrix for Chr (9 of 20)!, 0.205 mins elapsed.
## 2020-11-24 21:49:45 : Adding s1UI to PeakMatrix for Chr (10 of 20)!, 0.23 mins elapsed.
## 2020-11-24 21:49:46 : Adding s1UI to PeakMatrix for Chr (11 of 20)!, 0.254 mins elapsed.
## 2020-11-24 21:49:48 : Adding s1UI to PeakMatrix for Chr (12 of 20)!, 0.28 mins elapsed.
## 2020-11-24 21:49:49 : Adding s1UI to PeakMatrix for Chr (13 of 20)!, 0.303 mins elapsed.
## 2020-11-24 21:49:51 : Adding s1UI to PeakMatrix for Chr (14 of 20)!, 0.326 mins elapsed.
## 2020-11-24 21:49:52 : Adding s1UI to PeakMatrix for Chr (15 of 20)!, 0.349 mins elapsed.
## 2020-11-24 21:49:54 : Adding s1UI to PeakMatrix for Chr (16 of 20)!, 0.372 mins elapsed.
## 2020-11-24 21:49:55 : Adding s1UI to PeakMatrix for Chr (17 of 20)!, 0.395 mins elapsed.
## 2020-11-24 21:49:56 : Adding s1UI to PeakMatrix for Chr (18 of 20)!, 0.419 mins elapsed.
## 2020-11-24 21:49:58 : Adding s1UI to PeakMatrix for Chr (19 of 20)!, 0.441 mins elapsed.
## 2020-11-24 21:49:59 : Adding s1UI to PeakMatrix for Chr (20 of 20)!, 0.464 mins elapsed.
## ArchR logging successful to : ArchRLogs/ArchR-addPeakMatrix-cca78895fb1-Date-2020-11-24_Time-21-46-39.log

Motif enrichment

# add motifs
projPeaks <- addMotifAnnotations(ArchRProj = projPeaks, 
                                motifSet = "cisbp", 
                                name = "Motif",
                                force=TRUE)
## No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
## ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-cca73816a531-Date-2020-11-24_Time-21-50-01.log
## If there is an issue, please report to github with logFile!
## 2020-11-24 21:50:02 : Gettting Motif Set, Species : Mus musculus, 0.002 mins elapsed.
## Using version 2 motifs!
## 2020-11-24 21:50:04 : Finding Motif Positions with motifmatchr!, 0.032 mins elapsed.
## 2020-11-24 21:52:56 : Creating Motif Overlap Matrix, 2.899 mins elapsed.
## 2020-11-24 21:53:00 : Finished Getting Motif Info!, 2.963 mins elapsed.
## ArchR logging successful to : ArchRLogs/ArchR-addMotifAnnotations-cca73816a531-Date-2020-11-24_Time-21-50-01.log
# get markers
peakMarkersHBC <- getMarkerFeatures(
    ArchRProj = projPeaks, 
    useMatrix = "PeakMatrix", 
    groupBy = "clHBCMerged",
    bias = c("TSSEnrichment", "log10(nFrags)"),
    testMethod = "wilcoxon",
  verbose = FALSE)
## ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-cca756b750bb-Date-2020-11-24_Time-21-53-04.log
## If there is an issue, please report to github with logFile!
## MatrixClass = Sparse.Integer.Matrix
## ArchR logging successful to : ArchRLogs/ArchR-getMarkerFeatures-cca756b750bb-Date-2020-11-24_Time-21-53-04.log
peakMarkerListHBC <- getMarkers(peakMarkersHBC, cutOff = "FDR <= 0.01 & Log2FC >= 1.25")
saveRDS(markerList_HBCCl, file="../data/scATAC/markerList_atac_ArchR_hbcClusters.rds")

heatmapMarkers <- plotMarkerHeatmap(
  seMarker = peakMarkersHBC, 
  cutOff = "FDR <= 0.01 & Log2FC >= 1.25", 
  transpose = TRUE
)
## ArchR logging to : ArchRLogs/ArchR-plotMarkerHeatmap-cca71d155177-Date-2020-11-24_Time-21-54-16.log
## If there is an issue, please report to github with logFile!
## Identified 24150 markers!
## Preparing Main Heatmap..
## ArchR logging successful to : ArchRLogs/ArchR-plotMarkerHeatmap-cca71d155177-Date-2020-11-24_Time-21-54-16.log
ComplexHeatmap::draw(heatmapMarkers, heatmap_legend_side = "bot", annotation_legend_side = "bot")


## upregulated motifs 
motifsUp <- peakAnnoEnrichment(
    seMarker = peakMarkersHBC,
    ArchRProj = projPeaks,
    peakAnnotation = "Motif",
    cutOff = "FDR <= 0.05 & Log2FC >= 0.5"
  )
## ArchR logging to : ArchRLogs/ArchR-peakAnnoEnrichment-cca76bd8bab8-Date-2020-11-24_Time-21-54-23.log
## If there is an issue, please report to github with logFile!
## 2020-11-24 21:54:26 : Computing Enrichments 1 of 3, 0.049 mins elapsed.
## 2020-11-24 21:54:26 : Computing Enrichments 2 of 3, 0.058 mins elapsed.
## 2020-11-24 21:54:27 : Computing Enrichments 3 of 3, 0.08 mins elapsed.
## ArchR logging successful to : ArchRLogs/ArchR-peakAnnoEnrichment-cca76bd8bab8-Date-2020-11-24_Time-21-54-23.log
heatmapMotifsUp <- plotEnrichHeatmap(motifsUp, transpose = TRUE)
## ArchR logging to : ArchRLogs/ArchR-plotEnrichHeatmap-cca761cabd58-Date-2020-11-24_Time-21-54-28.log
## If there is an issue, please report to github with logFile!
## Adding Annotations..
## Preparing Main Heatmap..
pMotif <- ComplexHeatmap::draw(heatmapMotifsUp, heatmap_legend_side = "bot", annotation_legend_side = "bot")
pMotif

heatmapMotifsMatrix <- plotEnrichHeatmap(motifsUp, transpose = TRUE, returnMatrix = TRUE)
## ArchR logging to : ArchRLogs/ArchR-plotEnrichHeatmap-cca7683fbf16-Date-2020-11-24_Time-21-54-30.log
## If there is an issue, please report to github with logFile!
colnames(heatmapMotifsMatrix) <- unlist(lapply(strsplit(colnames(heatmapMotifsMatrix), split="_"), "[[", 1))

pMotif <- Heatmap(heatmapMotifsMatrix, 
        cluster_rows = FALSE,
        cluster_columns = FALSE,
        col = paletteContinuous(set = "comet", n = 100),
        column_names_gp = gpar(fontsize = 11),
        row_names_gp = gpar(fontsize = 13),
        heatmap_legend_param = list(title = "-log10 p-adj."))
pMotif


png("../plots/motifHeatmapHBCStates.png", width=10, height=7, units="in", res=300)
ComplexHeatmap::draw(heatmapMotifsUp, heatmap_legend_side = "bot", annotation_legend_side = "bot")
dev.off()
## quartz_off_screen 
##                 2

Export peak data for custom downstream analysis

useMatrix="PeakMatrix"
ArrowFiles <- getArrowFiles(projPeaks)
featureDF <- ArchR:::.getFeatureDF(head(ArrowFiles, 2), "PeakMatrix")
peakMat <- ArchR:::.getPartialMatrix(ArrowFiles, 
            featureDF = featureDF, threads = 1, useMatrix = "PeakMatrix", 
            cellNames = rownames(projPeaks@cellColData), progress = FALSE)
rownames(peakMat) <- featureDF$name
saveRDS(peakMat, file="../data/scATAC/peakMatArchrHbc_v2.rds")

Save ArchR project

saveArchRProject(ArchRProj = projPeaks, outputDirectory = "../data/scATAC/archR_samples_pairwise_v2", load = FALSE)

Composite plot

library(cowplot)
## 
## ********************************************************
## Note: As of version 1.0.0, cowplot does not change the
##   default ggplot2 theme anymore. To recover the previous
##   behavior, execute:
##   theme_set(theme_cowplot())
## ********************************************************
library(grid)

# DR of all cells
pCellType

# DR of HBCs
pstate 

# Barplot of injured vs uninjured in HBC states
pBar

# Motif enrichment
ComplexHeatmap::draw(Heatmap(heatmapMotifsMatrix))

# Composite
cowplot::plot_grid(pCellType + scale_color_manual(values = RColorBrewer::brewer.pal(9, "Set1")[c(2, 5, 9)]),
                   pstate,
                   pBar + theme_bw() + ylab("Cell count") + xlab("Treatment"),
                   grid::grid.grabExpr(ComplexHeatmap::draw(pMotif)),
                   nrow=2,
                   ncol=2,
                   labels=letters[1:4])
ggsave("../plots/figure3.png", width=12, height=9)